Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: KG483

Calculation Name: 1B77-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B77

Chain ID: A

ChEMBL ID:

UniProt ID: O80164

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2603927.279791
FMO2-HF: Nuclear repulsion 2515777.183025
FMO2-HF: Total energy -88150.096766
FMO2-MP2: Total energy -88407.18936


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-32.559-24.93230.207-11.483-26.355-0.093
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : 0.014
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3LEU0-0.040-0.0182.215-1.4450.7732.558-1.531-3.2450.004
4A4SER00.026-0.0044.6300.1100.199-0.001-0.017-0.0710.000
5A5LYS10.9080.9158.3330.4200.4200.0000.0000.0000.000
6A6ASP-1-0.907-0.94311.077-0.062-0.0620.0000.0000.0000.000
7A7THR0-0.021-0.0335.2450.1920.1920.0000.0000.0000.000
8A8ILE0-0.012-0.0087.2770.2080.2080.0000.0000.0000.000
9A9ALA0-0.026-0.0139.0910.0940.0940.0000.0000.0000.000
10A10ILE00.0120.00910.5460.0340.0340.0000.0000.0000.000
11A11LEU00.0070.0005.1470.0650.0650.0000.0000.0000.000
12A12LYS10.9240.9539.846-0.297-0.2970.0000.0000.0000.000
13A13ASN0-0.0140.01312.9360.0040.0040.0000.0000.0000.000
14A14PHE00.0540.02210.796-0.013-0.0130.0000.0000.0000.000
15A15ALA00.0230.02812.785-0.008-0.0080.0000.0000.0000.000
16A16SER0-0.089-0.04514.298-0.050-0.0500.0000.0000.0000.000
17A17ILE0-0.066-0.04116.309-0.051-0.0510.0000.0000.0000.000
18A18ASN0-0.057-0.04415.464-0.035-0.0350.0000.0000.0000.000
19A19SER00.0290.02714.9450.0330.0330.0000.0000.0000.000
20A20GLY00.0110.01713.3820.0400.0400.0000.0000.0000.000
21A21ILE0-0.050-0.0308.572-0.070-0.0700.0000.0000.0000.000
22A22LEU00.002-0.00510.0830.0630.0630.0000.0000.0000.000
23A23LEU0-0.0250.0023.457-0.545-0.2480.007-0.045-0.2600.000
24A24SER0-0.002-0.0386.9280.0330.0330.0000.0000.0000.000
25A25GLN0-0.067-0.0386.325-0.091-0.0910.0000.0000.0000.000
26A26GLY00.0090.0236.706-0.540-0.5400.0000.0000.0000.000
27A27LYS10.8530.9346.2430.7930.7930.0000.0000.0000.000
28A28PHE0-0.023-0.0227.986-0.219-0.2190.0000.0000.0000.000
29A29ILE00.0240.0326.1520.3500.3500.0000.0000.0000.000
30A30MET0-0.005-0.0019.072-0.271-0.2710.0000.0000.0000.000
31A31THR0-0.003-0.00111.6640.1200.1200.0000.0000.0000.000
32A32ARG10.8980.93414.061-0.456-0.4560.0000.0000.0000.000
33A33ALA00.0220.03917.7430.0340.0340.0000.0000.0000.000
34A34VAL00.0640.02620.096-0.008-0.0080.0000.0000.0000.000
35A35ASN00.0000.01921.8460.0020.0020.0000.0000.0000.000
36A36GLY0-0.006-0.00422.798-0.022-0.0220.0000.0000.0000.000
37A37THR0-0.009-0.02023.799-0.004-0.0040.0000.0000.0000.000
38A38THR00.0210.01319.937-0.018-0.0180.0000.0000.0000.000
39A39TYR0-0.051-0.06616.6220.0560.0560.0000.0000.0000.000
40A40ALA00.0150.00815.337-0.051-0.0510.0000.0000.0000.000
41A41GLU-1-0.853-0.89813.3830.4810.4810.0000.0000.0000.000
42A42ALA00.015-0.00511.586-0.086-0.0860.0000.0000.0000.000
43A43ASN0-0.0150.00611.0230.1630.1630.0000.0000.0000.000
44A44ILE00.003-0.0025.255-0.067-0.0670.0000.0000.0000.000
45A45SER00.0460.0108.9770.0510.0510.0000.0000.0000.000
46A46ASP-1-0.794-0.8393.868-1.082-0.9490.000-0.020-0.1140.000
47A47GLU-1-0.909-0.9824.4560.3130.547-0.001-0.048-0.1850.000
48A48ILE0-0.030-0.0122.351-2.751-2.8219.300-3.464-5.766-0.005
49A49ASP-1-0.822-0.9322.108-19.353-19.0039.283-1.821-7.812-0.067
50A50PHE0-0.017-0.0142.331-2.193-0.5981.562-0.683-2.474-0.001
51A51ASP-1-0.846-0.8985.0273.4973.7430.000-0.030-0.2170.000
52A52VAL0-0.011-0.0105.716-0.581-0.525-0.001-0.003-0.0530.000
53A53ALA0-0.0160.0028.3460.2070.2070.0000.0000.0000.000
54A54LEU00.0130.0096.862-0.121-0.1210.0000.0000.0000.000
55A55TYR00.0180.00111.083-0.119-0.1190.0000.0000.0000.000
56A56ASP-1-0.823-0.88913.8120.4850.4850.0000.0000.0000.000
57A57LEU00.0170.0088.2600.0270.0270.0000.0000.0000.000
58A58ASN00.0520.02411.237-0.036-0.0360.0000.0000.0000.000
59A59SER0-0.041-0.05013.745-0.081-0.0810.0000.0000.0000.000
60A60PHE00.0220.0215.313-0.066-0.0660.0000.0000.0000.000
61A61LEU00.005-0.0077.782-0.090-0.0900.0000.0000.0000.000
62A62SER0-0.079-0.05210.501-0.146-0.1460.0000.0000.0000.000
63A63ILE00.0110.02511.317-0.099-0.0990.0000.0000.0000.000
64A64LEU00.0130.0116.370-0.080-0.0800.0000.0000.0000.000
65A65SER0-0.143-0.07510.408-0.142-0.1420.0000.0000.0000.000
66A66LEU0-0.054-0.03113.452-0.042-0.0420.0000.0000.0000.000
67A67VAL0-0.041-0.00110.373-0.001-0.0010.0000.0000.0000.000
68A68SER0-0.019-0.03411.8400.0200.0200.0000.0000.0000.000
69A69ASP-1-0.861-0.93110.991-0.454-0.4540.0000.0000.0000.000
70A70ASP-1-0.971-0.9838.703-1.225-1.2250.0000.0000.0000.000
71A71ALA0-0.005-0.0037.570-0.377-0.3770.0000.0000.0000.000
72A72GLU-1-0.847-0.8972.615-10.572-8.7310.613-1.178-1.276-0.014
73A73ILE0-0.034-0.0332.147-1.5840.5081.204-0.996-2.3000.002
74A74SER00.0080.0112.7156.0224.4855.684-1.626-2.521-0.012
75A75MET0-0.0200.0024.6280.0030.086-0.001-0.021-0.0610.000
76A76HIS0-0.012-0.0137.454-0.427-0.4270.0000.0000.0000.000
77A77THR0-0.018-0.03110.7960.0340.0340.0000.0000.0000.000
78A78ASP-1-0.862-0.92213.9160.4460.4460.0000.0000.0000.000
79A79GLY0-0.0010.01212.4150.0090.0090.0000.0000.0000.000
80A80ASN0-0.051-0.03611.8090.2820.2820.0000.0000.0000.000
81A81ILE00.0180.0156.332-0.013-0.0130.0000.0000.0000.000
82A82LYS10.9200.9637.709-0.072-0.0720.0000.0000.0000.000
83A83ILE00.0060.0056.9060.2440.2440.0000.0000.0000.000
84A84ALA0-0.033-0.0287.434-0.027-0.0270.0000.0000.0000.000
85A85ASP-1-0.746-0.8438.856-0.615-0.6150.0000.0000.0000.000
86A86THR0-0.044-0.03311.643-0.003-0.0030.0000.0000.0000.000
87A87ARG10.9080.94414.2680.2690.2690.0000.0000.0000.000
88A88SER00.0010.00714.9560.0300.0300.0000.0000.0000.000
89A89THR0-0.033-0.02511.703-0.087-0.0870.0000.0000.0000.000
90A90VAL00.0040.01711.7470.0240.0240.0000.0000.0000.000
91A91TYR00.003-0.00311.0680.0320.0320.0000.0000.0000.000
92A92TRP00.004-0.00510.269-0.137-0.1370.0000.0000.0000.000
93A93PRO0-0.002-0.00111.7400.1170.1170.0000.0000.0000.000
94A94ALA00.0110.02011.0630.1780.1780.0000.0000.0000.000
95A95ALA0-0.046-0.02612.274-0.184-0.1840.0000.0000.0000.000
96A96ASP-1-0.784-0.86214.1360.6760.6760.0000.0000.0000.000
97A97LYS10.9570.96712.837-1.098-1.0980.0000.0000.0000.000
98A98SER0-0.095-0.06316.375-0.025-0.0250.0000.0000.0000.000
99A99THR0-0.070-0.04417.815-0.039-0.0390.0000.0000.0000.000
100A100ILE0-0.0050.00513.163-0.005-0.0050.0000.0000.0000.000
101A101VAL0-0.0040.00317.424-0.020-0.0200.0000.0000.0000.000
102A102PHE00.000-0.00914.2420.0580.0580.0000.0000.0000.000
103A103PRO0-0.0160.00214.502-0.070-0.0700.0000.0000.0000.000
104A104ASN0-0.001-0.01715.6350.0570.0570.0000.0000.0000.000
105A105LYS10.9390.96917.177-0.352-0.3520.0000.0000.0000.000
106A106PRO00.0700.03316.012-0.007-0.0070.0000.0000.0000.000
107A107ILE0-0.053-0.01717.664-0.043-0.0430.0000.0000.0000.000
108A108GLN0-0.003-0.00420.043-0.003-0.0030.0000.0000.0000.000
109A109PHE0-0.034-0.02223.382-0.007-0.0070.0000.0000.0000.000
110A110PRO00.0040.01725.472-0.009-0.0090.0000.0000.0000.000
111A111VAL0-0.005-0.00229.107-0.001-0.0010.0000.0000.0000.000
112A112ALA0-0.024-0.02130.4790.0000.0000.0000.0000.0000.000
113A113SER0-0.0050.00432.096-0.004-0.0040.0000.0000.0000.000
114A114VAL00.0070.00234.207-0.009-0.0090.0000.0000.0000.000
115A115ILE0-0.047-0.02530.7090.0100.0100.0000.0000.0000.000
116A116THR00.0400.03231.903-0.010-0.0100.0000.0000.0000.000
117A117GLU-1-0.842-0.90330.1020.0700.0700.0000.0000.0000.000
118A118ILE00.0130.02328.083-0.003-0.0030.0000.0000.0000.000
119A119LYS10.8840.93228.647-0.052-0.0520.0000.0000.0000.000
120A120ALA00.0270.00526.7000.0060.0060.0000.0000.0000.000
121A121GLU-1-0.947-0.97827.9550.0460.0460.0000.0000.0000.000
122A122ASP-1-0.825-0.91130.9460.0680.0680.0000.0000.0000.000
123A123LEU0-0.018-0.00624.6580.0040.0040.0000.0000.0000.000
124A124GLN00.0190.00528.0250.0070.0070.0000.0000.0000.000
125A125GLN0-0.0050.00329.0970.0040.0040.0000.0000.0000.000
126A126LEU00.0600.04130.5030.0010.0010.0000.0000.0000.000
127A127LEU00.0150.01025.4600.0030.0030.0000.0000.0000.000
128A128ARG10.8190.90827.997-0.079-0.0790.0000.0000.0000.000
129A129VAL00.0160.00231.8130.0000.0000.0000.0000.0000.000
130A130SER00.009-0.01232.153-0.001-0.0010.0000.0000.0000.000
131A131ARG10.9310.96726.863-0.137-0.1370.0000.0000.0000.000
132A132GLY0-0.0230.00133.596-0.001-0.0010.0000.0000.0000.000
133A133LEU0-0.026-0.00536.924-0.005-0.0050.0000.0000.0000.000
134A134GLN0-0.049-0.02636.452-0.003-0.0030.0000.0000.0000.000
135A135ILE0-0.0350.00334.6260.0000.0000.0000.0000.0000.000
136A136ASP-1-0.776-0.88533.5400.1300.1300.0000.0000.0000.000
137A137THR0-0.017-0.02233.3490.0080.0080.0000.0000.0000.000
138A138ILE0-0.006-0.00530.900-0.009-0.0090.0000.0000.0000.000
139A139ALA00.0100.00434.9660.0060.0060.0000.0000.0000.000
140A140ILE0-0.030-0.01131.551-0.006-0.0060.0000.0000.0000.000
141A141THR0-0.027-0.03736.2400.0010.0010.0000.0000.0000.000
142A142ASN0-0.0040.01439.6320.0010.0010.0000.0000.0000.000
143A143LYS10.8770.89941.991-0.059-0.0590.0000.0000.0000.000
144A144ASP-1-0.866-0.91744.5910.0530.0530.0000.0000.0000.000
145A145GLY00.0430.03245.588-0.002-0.0020.0000.0000.0000.000
146A146LYS10.8740.93241.515-0.049-0.0490.0000.0000.0000.000
147A147ILE0-0.0190.01535.9900.0030.0030.0000.0000.0000.000
148A148VAL0-0.027-0.02638.494-0.002-0.0020.0000.0000.0000.000
149A149ILE00.0080.00632.6150.0060.0060.0000.0000.0000.000
150A150ASN0-0.0040.01836.820-0.007-0.0070.0000.0000.0000.000
151A151GLY00.0360.00936.9900.0080.0080.0000.0000.0000.000
152A152TYR00.012-0.01337.642-0.008-0.0080.0000.0000.0000.000
153A153ASN0-0.009-0.01337.8810.0100.0100.0000.0000.0000.000
154A154LYS10.8640.91638.039-0.120-0.1200.0000.0000.0000.000
155A155VAL0-0.039-0.01538.624-0.003-0.0030.0000.0000.0000.000
156A156GLU-1-0.854-0.90541.2190.0820.0820.0000.0000.0000.000
157A157ASP-1-0.790-0.90543.1020.0780.0780.0000.0000.0000.000
158A158SER00.0180.01642.8790.0030.0030.0000.0000.0000.000
159A159GLY00.0070.00343.2290.0030.0030.0000.0000.0000.000
160A160LEU0-0.051-0.01138.4510.0000.0000.0000.0000.0000.000
161A161THR0-0.050-0.03643.015-0.004-0.0040.0000.0000.0000.000
162A162ARG10.8150.89545.054-0.080-0.0800.0000.0000.0000.000
163A163PRO0-0.0110.01642.2460.0030.0030.0000.0000.0000.000
164A164LYS10.8240.90540.734-0.090-0.0900.0000.0000.0000.000
165A165TYR0-0.036-0.04935.618-0.001-0.0010.0000.0000.0000.000
166A166SER0-0.018-0.01839.6160.0020.0020.0000.0000.0000.000
167A167LEU00.0040.02333.644-0.004-0.0040.0000.0000.0000.000
168A168THR0-0.001-0.00737.9000.0020.0020.0000.0000.0000.000
169A169LEU0-0.047-0.02533.1450.0000.0000.0000.0000.0000.000
170A170THR0-0.021-0.01735.081-0.005-0.0050.0000.0000.0000.000
171A171ASP-1-0.846-0.90637.9410.0480.0480.0000.0000.0000.000
172A172TYR0-0.075-0.07039.7180.0040.0040.0000.0000.0000.000
173A173ASP-1-0.894-0.95041.8200.0470.0470.0000.0000.0000.000
174A174GLY0-0.070-0.03642.774-0.001-0.0010.0000.0000.0000.000
175A175SER0-0.006-0.00543.728-0.002-0.0020.0000.0000.0000.000
176A176ASN0-0.048-0.02141.904-0.001-0.0010.0000.0000.0000.000
177A177ASN00.0220.02443.552-0.003-0.0030.0000.0000.0000.000
178A178PHE00.024-0.00838.0730.0040.0040.0000.0000.0000.000
179A179ASN0-0.0020.01539.517-0.006-0.0060.0000.0000.0000.000
180A180PHE00.0340.00034.1400.0030.0030.0000.0000.0000.000
181A181VAL00.0250.01735.284-0.002-0.0020.0000.0000.0000.000
182A182ILE00.005-0.00428.9670.0110.0110.0000.0000.0000.000
183A183ASN00.0950.05929.428-0.016-0.0160.0000.0000.0000.000
184A184MET0-0.016-0.00429.0550.0100.0100.0000.0000.0000.000
185A185ALA0-0.018-0.00727.7530.0070.0070.0000.0000.0000.000
186A186ASN0-0.049-0.04324.7180.0080.0080.0000.0000.0000.000
187A187MET00.0240.01323.9450.0190.0190.0000.0000.0000.000
188A188LYS10.8320.92720.121-0.323-0.3230.0000.0000.0000.000
189A189ILE0-0.0100.01219.9040.0250.0250.0000.0000.0000.000
190A190GLN00.0030.01415.7180.0110.0110.0000.0000.0000.000
191A191PRO00.001-0.00720.188-0.009-0.0090.0000.0000.0000.000
192A192GLY00.0560.02021.490-0.002-0.0020.0000.0000.0000.000
193A193ASN0-0.014-0.00223.6200.0030.0030.0000.0000.0000.000
194A194TYR0-0.047-0.04120.6120.0130.0130.0000.0000.0000.000
195A195LYS10.9010.94725.500-0.127-0.1270.0000.0000.0000.000
196A196VAL0-0.024-0.03826.3970.0150.0150.0000.0000.0000.000
197A197MET0-0.047-0.00624.948-0.013-0.0130.0000.0000.0000.000
198A198LEU00.0340.01629.0130.0150.0150.0000.0000.0000.000
199A199TRP00.031-0.00130.748-0.002-0.0020.0000.0000.0000.000
200A200GLY00.0810.03332.6580.0070.0070.0000.0000.0000.000
201A201ALA0-0.043-0.01535.259-0.007-0.0070.0000.0000.0000.000
202A202GLY00.0190.01036.9680.0050.0050.0000.0000.0000.000
203A203ASP-1-0.817-0.89037.1120.1420.1420.0000.0000.0000.000
204A204LYS10.7960.89132.868-0.144-0.1440.0000.0000.0000.000
205A205VAL00.0310.01133.004-0.008-0.0080.0000.0000.0000.000
206A206ALA0-0.020-0.01227.5900.0140.0140.0000.0000.0000.000
207A207ALA00.0250.02127.679-0.015-0.0150.0000.0000.0000.000
208A208LYS10.8950.94320.823-0.210-0.2100.0000.0000.0000.000
209A209PHE0-0.0090.00223.279-0.022-0.0220.0000.0000.0000.000
210A210GLU-1-0.805-0.89821.2930.1870.1870.0000.0000.0000.000
211A211SER00.0470.03919.783-0.024-0.0240.0000.0000.0000.000
212A212SER0-0.048-0.03520.1190.0160.0160.0000.0000.0000.000
213A213GLN0-0.003-0.00115.7710.0150.0150.0000.0000.0000.000
214A214VAL00.0180.01514.4570.0410.0410.0000.0000.0000.000
215A215SER00.0070.00416.732-0.050-0.0500.0000.0000.0000.000
216A216TYR0-0.003-0.03117.2450.0310.0310.0000.0000.0000.000
217A217VAL0-0.031-0.01620.333-0.028-0.0280.0000.0000.0000.000
218A218ILE0-0.035-0.02022.6400.0250.0250.0000.0000.0000.000
219A219ALA0-0.012-0.00125.154-0.016-0.0160.0000.0000.0000.000
220A220MET0-0.057-0.01227.927-0.004-0.0040.0000.0000.0000.000
221A221GLU-1-0.872-0.94631.3590.1800.1800.0000.0000.0000.000
222A222ALA00.0100.00234.262-0.005-0.0050.0000.0000.0000.000
223A223ASP-1-0.894-0.94137.1710.1190.1190.0000.0000.0000.000
224A224SER0-0.020-0.01035.642-0.006-0.0060.0000.0000.0000.000
225A225THR0-0.030-0.01838.273-0.003-0.0030.0000.0000.0000.000
226A226HIS0-0.089-0.05438.479-0.003-0.0030.0000.0000.0000.000
227A227ASP-1-0.803-0.88241.0070.0760.0760.0000.0000.0000.000
228A228PHE0-0.042-0.01138.675-0.001-0.0010.0000.0000.0000.000